Optical analyte sensor

ABSTRACT

A waveguide sensor capable of direct, real-time detection and monitoring of analytes in the vicinity of the waveguide surface without requiring the tagging or labeling of the analyte, is described. Analytic and numerical calculations have predicted that by locally detecting either changes in the evanescent field or changes in the light coupled out of the waveguide as a result of the presence of the analyte, high detection sensitivity will be able to be achieved.

RELATED CASES

The present application claims the benefit of provisional patentapplication Ser. No. 60/670,939 for “Multi-Analyte Optical Sensor” byKevin L. Lear et al., filed on Apr. 12, 2005, which application ishereby incorporated by reference herein for all that it discloses andteaches.

STATEMENT REGARDING FEDERAL RIGHTS

This invention was made with government support under Grant No. EB 00726awarded by the U.S. National Institutes of Health to Colorado StateUniversity. The government has certain rights in the invention.

FIELD OF THE INVENTION

The present invention relates generally to analyte detection and, moreparticularly, to the use of evanescent and coupled electromagnetic wavesfrom optical waveguide structures for sensing analytes.

BACKGROUND OF THE INVENTION

The low absorption loss, high sensitivity, and flexible light detectionabilities of integrated optical waveguide analyte sensors make themsuitable for many practical biological and chemical environments. Suchanalyte sensors include attenuation total reflection (ATR) [See, e.g.,J. E. Midwinter in “On the use of optical waveguide techniques forinternal reflection spectroscopy,” IEEE J. Quantum Electron. 7, pp.330-344 (1971)], Raman scattering waveguide (RSW) [See, e.g., Y. Levy etal. in “Raman scattering of thin films as a waveguide,” Opt Commune 11,pp. 66-69 (1974)], and florescence spectrometry [See, e.g., W. M.Reichert et al. in “Excitation of fluorescent emission from solutions atthe surface of polymer thin-film waveguides: an integrated opticstechnique for the sensing of fluorescence at the polymer/solutioninterface,” Appl. Spectrosc. 41, pp. 636-640 (1987); U.S. PatentApplication Publication No. US200610019244, Jan. 26, 2006 for “PlanarOptical Waveguide Based Sandwich Assay Sensors And Processes for TheDetection Of Biological Targets Including Protein Markers, Pathogens AndCellular Debris”; and U.S. Patent Application Publication No. US2003/0132406, Jul. 17, 2003 for “Sensor Element For Optically DetectingChemical Or Biochemical Analytes.”].

Analytes are substances or chemical constituents undergoing analysis.Florescence-based waveguide analyte sensors rely on the use ofexcitation of a tag or label, such as a florescent dye, by excitationlight guided in the waveguide with subsequent detection of florescenceat a wavelength different from the wavelength of the excitation.Analytes may be dissolved in appropriate solvents therefor or may besuspended in fluids.

Present non-florescence-based optical waveguide analyte sensors rely onthe optical properties of an analyte, such as refractive index orabsorption, to alter the phase or amplitude of the light propagating inthe waveguide. Included are an optical waveguide core; an opticalwaveguide lower cladding having a refractive index lower than that forthe core; a photodetector; and optionally a substrate for additionalmechanical support. Light is directed through the core, and evanescentportions of the optical field penetrate into regions near the coreincluding the analyte and the lower cladding. The photodetector ispositioned at the end of the waveguide to intercept the intensity oflight traveling in the core which is responsive to changes in theevanescent field resulting from the interaction between the evanescentfield and the analyte in contact with a portion of the exterior of thewaveguide [See, e.g., U.S. Pat. No. 5,144,690 for “Optical Fiber SensorWith Localized Sensing Regions” which issued to Lawrence H. Domash onSep. 1, 1992; and U.S. Pat. No. 5,991,479 for “Distributed Fiber OpticSensors And Systems” which issued to Marcos Y. Kleinerman on Nov. 23,1999.].

Interferometric waveguide structures including Mach-Zehnderinterferometers consisting of multiple waveguides that are coupled attwo or more points along their lengths may be employed; however, aphotodetector positioned at the terminus of one or more of thewaveguides is used to detect the light propagated in the core. Light maybe introduced into the waveguide using either end-fire, prism, orgrating coupling techniques that are well known to those skilled in theart.

An alternative is to use a prism to permit the light to exit thewaveguide away from the sensor region and direct the light coupled outthrough the prism to a detector. Such configurations permit only oneanalyte to be sensed with each waveguide.

Conventional ATR and RSW waveguide analyte sensors are often limited inthe number of analytes that can be simultaneously detected by onesensor, and require complex sample preparation; that is, the large sizeand non-local detection characteristic of these sensors diminishes theirapplicability to complex and multiple analyte environments.Additionally, sensors using florescence spectrometry require that thetarget samples be prepared with chemically specific dyes or labels whichincreases the complexity and overall cost for analyses.

Accordingly, it is an object of the present invention to provide anapparatus and method for detecting analytes,

It is another object of the invention to provide an apparatus and methodfor simultaneously or individually detecting multiple analytes.

It is yet another object of the invention to provide and apparatus andmethod for detecting multiple analytes without requiring markers, suchas fluorescent tags, attached to the analytes.

Additional objects, advantages and novel features of the invention willbe set forth in part in the description that follows, and in part willbecome apparent to those skilled in the art upon examination of thefollowing or may be learned by practice of the invention, The objectsand advantages of the invention may be realized and attained by means ofthe instrumentalities and combinations particularly pointed out in theappended claims.

SUMMARY OF THE INVENTION

The present invention overcomes the disadvantages and limitations of theprior art by allowing at least one light detector to be placed along thelength of an optical waveguide, thereby permitting direct localdetection of evanescent radiation emanating transversely from thewaveguide core or light coupled out of the waveguide core into regionslocated alongside the waveguide responsive to analytes in the vicinityof the surface thereof, rather than directing the propagating field inthe waveguide onto a detector disposed at the end of the waveguide.Hereinafter, optical guide, guide and waveguide are used interchangeablyand may include optical waveguides, optical fibers, and the like, asexamples. For bioassays, the analyte, also known as the target, mayinclude antigens, single-strands of DNA (ssDNA), proteins, and the likeas examples, and the probe species which is immobilized in the vicinityof at least one region of the surface of the optical waveguide, mayinclude antibodies, complementary single-strands of DNA, aptamers,proteins, and the like, as examples, which may specifically bind to theprobe species. More generally, analytes may include gases and liquidscontaining materials under investigation as solutes or as suspensions.

To achieve the foregoing and other objects, and in accordance with thepurposes of the present invention, as embodied and broadly describedherein, the analyte sensor or detector hereof includes in combination: alight source for generating light having a chosen wavelength or band ofwavelengths; an optical guide having a surface and an axis, capable ofreceiving light from the light source and for transmitting the lightalong the axis, and having at least one region on the surface thereofwherein an evanescent field is generated substantially perpendicular tothe axis of the guide such that the evanescent field extends from thesurface within the at least one region; and at least one detectordisposed in the vicinity of the at least one region where the evanescentfield extends from the surface of the guide, for detecting the intensityof the evanescent field, whereby the analyte modifies the distributionof the evanescent field thereby changing the intensity thereof detectedby the at least one detector.

In another aspect of the present invention, in accordance with itsobjects and purposes, the method for sensing or detecting an analytehereof includes the steps of: introducing light having a chosenwavelength or band of wavelengths into an optical guide having a surfaceand an axis, capable of transmitting light along the axis, and having atleast one region on the surface thereof wherein an evanescent field isgenerated substantially perpendicular to the axis of the guide such thatthe evanescent field extends from the surface within the at least oneregion; contacting the analyte with the evanescent field extending fromthe at least one region, whereby the analyte modifies the distributionof the evanescent field thereby changing the intensity thereof; anddetecting the change of intensity of the evanescent field extending fromthe surface in the vicinity of the at least one region.

In yet another aspect of the present invention, in accordance with itsobjects and purposes, the analyte sensor or detector hereof includes incombination: a light source for generating light having a chosenwavelength or band of wavelengths; an optical guide having a surface andan axis, capable of receiving light from the light source and fortransmitting the light along the axis, and having at least one region onthe surface thereof wherein the index of refraction in the vicinity ofthe surface is modified by the presence of the analyte, and theintensity of light coupled out of the optical guide is changed; and atleast one detector disposed on the side of the guide in the vicinity ofthe at least one region from which the light is coupled out of theoptical guide, for detecting the change in intensity of the lightcoupled out of the optical guide at the chosen wavelength or band ofwavelengths.

In still another aspect of the present invention, in accordance with itsobjects and purposes, the method for sensing or detecting an analytehereof includes the steps of: introducing light having a chosenwavelength of band of wavelengths into an optical guide having a surfaceand an axis, capable of transmitting light along the axis, and having atleast one region in the vicinity of the surface thereof wherein therefractive index thereof is altered by the presence of the analyte;placing the analyte in the vicinity of the at least one region of thesurface, whereby the intensity of light coupled out of the optical guideis changed as a result of the presence of the analyte; and detecting thechange of intensity of the light coupled out of the guide at the chosenwavelength or band of wavelengths in the vicinity of the at least oneregion.

Benefits and advantages of the present invention include, but are notlimited to, the capability of simultaneous detection of multipleanalytes without requiring fluorescent or other marker labeling using awaveguide sensor having a thin core region that creates a sufficientlylarge evanescent field capable of interacting with multiple adlayerregions which interaction can be locally detected near the sites of theadlayers. Detection of multiple antigens or pathogens using a compactsensor permits the present sensor to be useful for complex medical,security, and environmental applications.

BRIEF DESCRIPTION OF THE DRAWINGS

The accompanying drawings, which are incorporated in and form a part ofthe specification, illustrate several embodiments of the presentinvention and, together with the description, serve to explain theprinciples of the invention. In the drawings:

FIG. 1 is a schematic representation of a cross-sectional side view ofone embodiment of the apparatus of the present invention illustratingthe position of the photodetector relative to the core of the waveguideand the analyte.

FIG. 2A shows a theoretical depiction of the power in the evanescentfield detected by a photodetector for a detection system having probematerials deposited onto the surface of the waveguide core illustratedin FIG. 1 hereof, but without a target bound to the probe, while FIG. 2Bis a depiction of the power in the evanescent field detected by thephotodetector after the probe is exposed to the appropriatetarget-containing solution or suspension, respectively, and targetbinding takes place, the difference between the two detected powerlevels being responsive to the optical characteristics of the boundtarget layer.

FIG. 3 is a graph of the theoretical contour plot of detected evanescentfield power difference as a function of core and lower claddingrefractive indices.

FIG. 4 is a graph of the theoretical normalized detected evanescentfield power difference as a function of the distance between the core ofthe waveguide and the photodetector.

FIG. 5 is a graph of the theoretical normalized detected evanescentfield power difference as a function of the thickness of the adlayer.

FIG. 6 is a graph of the ratio of theoretical detected evanescent fieldpower for finite length evanescent field detector segments normalized bythe theoretical detected evanescent field power for a semi-infinitedetector as a function of adlayer length.

FIG. 7 is a graph of the theoretical signal-to-noise ratio for differentadlayer thicknesses and detector-to-core distances.

FIG. 8A is a schematic representation of a cross-sectional side view ofan embodiment of the apparatus of the present invention illustratingmultiple sensing locations for detecting a multiplicity of analytes, ormaking several measurements of the same analyte, that bind tocorresponding recognition layers located on the surface of thewaveguide, while FIG. 8B is a schematic representation of a top viewthereof.

DETAILED DESCRIPTION OF THE INVENTION

Briefly, the present invention includes a waveguide sensor that forsimultaneously detecting multiple analytes. The process of detectiondoes not require labeling of the analytes with fluorescent or othertags. The waveguide has a thin core that can create large evanescentfields which can be detected in the region of the evanescent field andwhich fields interact with adlayer regions through which the evanescentfields pass, thereby generating changes in the field intensity.

In another embodiment of the invention, light may be coupled out of thewaveguide in amounts which vary as a result of the interaction of thecore with the analyte.

It has been theoretically determined by the present inventors that thepower distribution of the electromagnetic field in the waveguide isdependent on the thickness of adlayers which are assumed, in thecalculations which follow, to be target species bound to patches ofprobe species immobilized in the vicinity of the waveguide surface. Toquantitatively calculate the detected power difference before and afterthe target/probe binding, waveguide parameters were investigated usingthe beam propagation method (BPM) and the finite difference time domain(FDTD) method electromagnetic field simulations.

Numerical modeling shows that high sensitivity can be achieved when asingle mode asymmetric waveguide structure is operating near to thefundamental mode cutoff region. The cutoff region occurs where there areno longer any bound modes propagating with total internal reflection,and is a function of wavelength, layer dimensions (thickness), and theindices of refraction of the core and cladding layers. Cutoff isspecific to the waveguide asymmetry, symmetric waveguides theoreticallyhaving no cutoff value. Although a waveguide does not need to beoperated close to cutoff to function in accordance with the presentinvention, nor does it necessarily require asymmetry, the sensitivity tochanges is maximized close to cutoff where a large evanescent field isgenerated and changes in adlayer thickness and width can strongly afterthe electromagnetic field distribution. Such changes can be locallydetected by an array of p-i-n (PIN), metal-semiconductor-metal (MSM), orother types of photodiodes in the lower cladding region, as an example.Near-field scanning optical microscopy (NSOM) has been used to detectthe evanescent field in the upper cladding of the waveguide [See, e.g.,Guangwei Yuan et al. in “Direct Imaging of Transient Interference in aSingle-Mode Waveguide Using Near-Field Scanning Optical Microscopy,”IEEE Photonics Tech, Lett. 17, pp. 2382-2385 (2005); and Guangwei Yuanet al. in “Initial Demonstration of a Local, Evanescent, Array CoupledBiosensor,” 4^(th) IEEE International Conference on Sensors, paperB4P-G, Irvine, Calif., Oct. 31, 2005.]. Either detection method can beused to monitor the analyte binding in real time. In addition, thesensor of the present invention will be able to sense multiple regionsof different antibody patches placed on the waveguide.

By treating the sensor structure as a number of abrupt adiayers on thesurface of a waveguide which can be analyzed as corrugations ordiscontinuities, rigorous analytical solutions have been developed formode coupling [See, e.g., A. Hardy, “Exact derivation of the couplingcoefficient in corrugated waveguides with rectangular tooth shape,” IEEEJ. Quant. Electron., 20, pp. 1132-1139 (1984); and N. Morita, “Arigorous analytical solution to abrupt dielectric waveguidediscontinuities”, IEEE Trans. Microwave Theory and Tech, 39, pp.1272-1278 (1991).]. The behavior of the electromagnetic field after anabrupt discontinuity has been derived by the present inventors usingthis approach and by using commercially available computer simulationtools including BPM and FDTD modeling of optical waveguide structures.

The intensity of evanescent fields decays exponentially in thetransverse direction. In general, the evanescent field remains strongapproximately 1 μm into gases having low indices of refraction or liquidanalytes, and approximately 2 to 3 μm into higher index of refractiondetectors. Therefore, although the extents of such fields are quitevariable, they may be readily determined for various configurations ofcore and cladding thicknesses, core and cladding refractive indices, andwavelength using established methods known to those skilled in the art.In an embodiment of the present invention, the analyte may be bound towithin about 100 nm of the optical waveguide, and the photodetector isplaced within approximately 1 μm of the waveguide. A lower cladding waspresent in this embodiment.

Reference will now be made in detail to the present preferredembodiments of the present invention, examples of which are illustratedin the accompanying drawings. In what follows, identical callouts willbe used to identify similar or identical structure. Turning now to FIG.1, a schematic representation of a cross-sectional side view of oneembodiment of the apparatus, 10, of the present invention is shown.Photodetector, 12, is located on the side of lower cladding layer, 14,away from core, 16, and has a surface, 18, substantially parallel tosurface, 20, of core 16. Light, 21, having a chosen wavelength isdirected into one end of core 16 using standard procedures, such asendfire coupling, prism coupling or grating coupling, as examples (notshown in FIG. 1) from light source, 22, and any remaining light which iseither not absorbed or coupled out of core 16, exits through end, 23.Single mode and multimode lasers, light-emitting diodes, and otherrelatively narrow continuum light sources may be used, althoughsingle-mode lasers may be advantageous for end-fire or higher gratingcoupling efficiency because of their better focusing characteristics.The intensity of guided light 22 is observable by photodetector 12, inaccordance with the teachings of the present invention, as a result ofthe evanescent field associated with the optical field of the lighttransmitted through core 16 extending through lower cladding 14 intodetector layer 12. Core layer 16 is chosen to have a larger refractiveindex than lower cladding 14. The field would typically be evanescent inlower cladding 14, but could become propagating in detector layer 12 ifthe refractive index of the detector layer is sufficiently high. Thisarrangement may also be considered to be evanescent coupling of thelight in core 16 to a secondary lossy waveguide with the detector layer12 serving as the core of the secondary lossy waveguide.

Another embodiment of detector layer 12 of the present invention iswhere the detector layer is disposed on the same side of core 16 asanalyte 24. As an example, the detector may include a lower cladding 14,core 16, analyte 24, and detector layer 12, in that order. Other layersmight be included intermediate to these layers so long as the evanescentfield reaching the detector layer is sufficient to permit adequatedetection of changes in the field distribution due to the presence orabsence of adlayers formed on surfaces adjacent to the analyte region.Yet another embodiment would place detector layer 12 intermediatebetween core 16 and analyte 24. It is to be noted that placing detector12 intermediate core 16 and analyte 24 requires that detector 12 issufficiently thin such that the evanescent field can pass therethrough;however, for detectors disposed on the opposite side of core 16 fromanalyte 24, or where analyte 24 is disposed between core 16 and detector12, either thick or thin detectors may be employed.

Thicknesses and materials of core 16 and lower cladding layer 14 arechosen such that a chosen amount of light coupling to photodetectorlayer 12 is generated relative to the optical properties of analyte, 24.Analyte 24 may be a gas, a liquid, a solution, or a porous solid thatadmits a gas or liquid. The analyte or changes in the analyte aredetected by virtue of the changes in refractive index of the analyteeither as a whole or in a portion of the analyte, in the region of thecore. In the anti-guiding or leaky-mode operation of the opticalwaveguide, core layer 16 is chosen to have an index of refraction lowerthan that for analyte 24. In such a situation, light 22 is coupled intoa propagating field in analyte 24 in an amount dependent upon therefractive index of the analyte. Higher analyte refractive indicesdecrease the amount of light coupled into the analyte for thisanti-guiding configuration.

Core material 16 may also be chosen to have a higher refractive indexthan analyte 24. In this situation, only an evanescent portion of theoptical field is present in the analyte; however, the refractive indexof the analyte can alter the relative distribution of light between thepropagating field 22 in waveguide core 16 and the evanescent field inlower cladding 14. An increase in the refractive index of the analyteincreases the amount of evanescent field in the analyte and decreasesthe amount of evanescent field in the lower cladding and detector layerswhen positioned as shown in FIG. 1. As an example of a layer structureuseful with an aqueous analyte 24 having an approximate refractive indexof 1.33 is a silicon oxynitride core 16 having a refractive indexranging between 1.45 and 2.1, depending on its stoichiometry, and asilicon dioxide lower cladding having a refractive index ofapproximately 1.45. The core layer thickness can be betweenapproximately 20 and 200 nm, with smaller values producing largerevanescent fields. The thickness of lower cladding 14 may be betweenapproximately 100 and 2000 nm depending on the desired strength of fieldcoupling to detector layer 12.

It should be mentioned that the waveguide core may have a rectangular,as described hereinabove, circular, as would be the situation for anoptical fiber, elliptical, or other cross section. It may beadvantageous to limit the lateral extent of the core layer so that thewaveguide operates in a single transverse guided mode. The effectivelateral index profile may be controlled by either completely orpartially etching or otherwise changing the thickness of the high indexof refraction core layer in regions outside the waveguide core.Waveguides having lateral definition are known as rib or ridgewaveguides.

Detector layer 12 may be composed of a material that is absorbing at thewavelength of light guided in the waveguide. The wavelength of the lightused can range from the ultra-violet through the visible to the infrareddepending on the absorption properties of the detector. For example,silicon can be used as a detector element for wavelengths less thanapproximately 1100 nm. Other possible detector materials include, butare not limited to, direct-gap and indirect-gap inorganic and organicsemiconductors in single crystal, polycrystalline, and amorphous forms.Other suitable photodetectors include photodiodes containingmetal-semiconductor, p-n, or p-i-n junctions, photoconductors, andbolometers, as examples. Wavelengths generated by laser diodes atapproximately 1550 nm, 1300 nm, 980 nm, 850 nm, 780 nm, 650 nm, and 400nm, as examples, are convenient.

Many suitable detector materials 12, such as inorganic semiconductors,will have refractive indices greater than those of lower cladding 14 andoften greater than that for core 16. In such situations, core layer 16and detector layer 12 function as parallel waveguides that areevanescently coupled through lower cladding layer 14 although theabsorbing detector waveguide would be considered lossy. The couplingcoefficients between the two waveguides including the dependence on therefractive indices and thicknesses of core 16, lower cladding 14, anddetector 12 layers can be calculated to determine the amount of powercoupled into the detector layer. As stated hereinabove, analyticalapproximations may be employed to provide a rough calculation of thecoupling coefficients following methods presented in textbooks onoptical waveguides such as L. Coldren and S. Corzine [See, e.g., DiodeLasers and Photonic Integrated Circuits, New York, Wiley (1995), and thereferences cited therein], More complete or accurate results forcoupling power into the detector layers 12 may be obtained fromnumerical simulations including those performed using commercial opticalwaveguide modeling software available from vendors including RSoft. Asubstantial amount of power may be coupled into the working length ofthe detector including multiple segments in the case that the detectoris segmented as described hereinbelow. It may be advantageous to controlthe amount of power coupled to the detectors so that the tradeoff isappropriately balanced between providing sufficient signal to thedetector and maintaining sufficiently low loss in the waveguide topermit the mode to propagate through a large number of detectionregions. The amount of coupling for a particular core, cladding anddetector layer design parameters may be usefully quantified in terms ofthe absorption loss, α, in units of cm⁻¹. If the combined length of thedetectors along a waveguide segment is denoted as L, then a usefulembodiment of the present invention would be given approximately by thecondition 0.1<αL<2.

It should be mentioned that in the event that multiple analytes or morethan one measurement of the same analyte are to be detected by opticalanalyte sensor 10, detector 12 is better segmented by conductivity alongthe length of optical guide 16, than being segmented by refractiveindex. However, even for a detector having minor perturbations in itsindex of refraction, it is believed by the present inventors that therewill be acceptable coupling to the waveguide.

In the situation where the refractive index of the core is greater thanthe refractive index of the analyte 24, lower cladding material 14 maybe chosen to have an index of refraction higher than that of analyte 24,but lower than that of the core 16. This is a consequence of the rarityof materials having indices of refraction less than the index ofrefraction of water (<1.33). There is an advantage of using evanescencein the lower cladding to maintain the coupling to the detector layersufficiently low that the bulk of the power is not significantly coupledinto detector layer 12, as described hereinabove.

This asymmetric waveguide structure can be designed to operate near thecut-off by proper choice of the core thickness (between 10 and 500 nm)in order to enhance changes in the coupling to the detector as a resultof small changes in the analyte's refractive index. As an example, sucha structure will result when the analyte 24 is an aqueous solutionhaving a refractive index of approximately 1.33, and the lower cladding14 is silicon dioxide having a refractive index of 1.45. It has beendetermined by the present inventors that use of a core having dimensionsof 100 nm thickness and 2 μm width (As an example, SiO_(x)N_(y) havingan refractive index of about 1.8, where the subscripts x and y indicatethat the stoichiometry of the film may be adjusted to achieve thedesired index of refraction.), and a 500 nm thickness for the SiO₂ lowercladding, that the guided mode is close to cutoff, with or without thepresence of the adlayer, thereby providing better sensor response. Itshould be mentioned that if lower analyte detector sensitivity can beaccepted, a 200 nm core thickness has advantages in manufacturing of thedevice. Reducing the thickness and decreasing the refractive index ofcore 16 both generally cause an asymmetric waveguide to be closer tocut-off. As such, there is a tradeoff between core thickness andrefractive index when designing the waveguide to be close to cut-off.The choice of nominal core thickness and refractive index will be guidedby the ability of manufacturing processes to control the thickness andmaterial composition, including as appropriate the stoichiometry, of thecore which in turn affects the refractive index of the core.

Turning to FIG. 2A and again to FIG. 1, it is assumed that analyte 24 isan aqueous analyte having a refractive index of n_(u)=1.33 that servesas the upper cladding of waveguide core 16. As stated hereinabove,materials for waveguide core 16 can be chosen within certain constraintsto have an index n_(c). Lower cladding 14 is chosen to have index n₁. InFIG. 2A, detector 12 is shown detached from surface 18 of lower cladding14, by a distance, S. Shown also in FIG. 2A is probe layer, 26,immobilized on surface, 28, of core 16. The core thickness beforebinding is shown as d₁; after binding with target species, 30, inaqueous analyte 24, the core thickness becomes d₂ (d₁˜110 nm, and 110nm<d₂<200 nm have been simulated). Bare waveguide core 16 thickness isd, and any adlayer (target/probe layer), 32, thickness is d_(a). Theprobe and/or target films generally have a refractive index n_(a)=1.45,since such films are principally proteins. When the target is bound, thefield profile shifts such that there is less overlap with the detector.That is, target binding changes the evanescent decay constant from q₁ toq₂ (measured in cm⁻¹, as an example), with q₂>q₁. Values of q₁ and q₂may be calculated from the details of the refractive indices of thelayers including the adlayer, using well-known numerical procedures,such as those mentioned hereinabove.

In order to have only one bound mode, there is one unique solution forthe propagation constant β=kn_(e), where k is the free space wave vectorand n_(e) is effective refractive index. Other conditions such asn_(c)>n_(e)>n_(u), n_(i), are required. A large core thickness will makethe waveguide multimode, whereas a small core thickness may makeefficient light coupling more difficult. For purposes of illustration,the waveguide core thickness has been chosen to be 100 nm. Neglectingthe longitudinal dependence, the transverse electromagnetic fieldprofile of the TE₀ mode can be expressed as:

$\begin{matrix}{{E^{t}(x)} = \{ {\begin{matrix}{{A \cdot ^{{- p} \cdot x}},} & {x < 0} \\{{B \cdot {f( {x,\beta} )}},} & {0 \leq x \leq d} \\{{C \cdot ^{q \cdot x}},} & {d < x}\end{matrix},} } & (1)\end{matrix}$

where β is the propagation constant.

The function, f(x,β) is related to the geometry of the guided layer andmust meet the boundary conditions. It is approximately sinusoidal forcore layers having constant index of refraction. Other importantparameters include the penetration depth 1/p=1/√{square root over(β²−k²·n_(u) ²)} and 1/q=1/√{square root over (β²−k²·n_(i) ²)} in theupper and lower cladding regions, respectively. Larger penetrationdepths result in more power being confined in the evanescent field. InFIG. 2A, P₁ denotes the detected power before the antigen-antibodybinding, whereas P₂, in FIG. 2B denotes the detected power after theantigen-antibody binding. In order to find the relative power change,some approximations must be made. As described hereinabove, this systemis an asymmetric waveguide operating near the fundamental mode cut-offregion. The penetration depth in the lower cladding is much larger thanthat in the upper cladding region and the waveguide core thickness; thatis, 1/q>>1/p>>d for this configuration. Therefore, the normalizeddetected power difference can be approximately expressed as:

$\begin{matrix}{{\Delta \; {P/P_{0}}} = {{\eta \cdot \frac{P_{1} - P_{0}}{P_{1}}} \approx {1 - {\frac{p_{1}}{p_{2}}^{{- 2} \cdot {({q_{1} - q_{2}})} \cdot {({S - {d/2}})}}}}}} & (2)\end{matrix}$

In Equation 2, p₁ and p₂ are associated with penetration depth in theupper cladding before and after binding, respectively. Similarly, q₁ andq₂ are associated with penetration depth in the lower cladding beforeand after binding, respectively. The mode coupling efficiency, η, isclose to unity in most situations. However, in a rigorous derivation, ηmay have a value less than unity. Since the sensor regions can betreated as waveguide corrugations or discontinuities, the theoreticalmethods in references [See, e.g., A. Hardy: and N. Morita, supra.] arevalid for calculating η. In general, the theoretically calculated η isbetween 0.96 and 0.99, while the BPM simulated result η is between 0.95and 0.99.

The analytic calculations provide useful results for layers that aresufficiently long that transients induced by the edges have died out,and provide useful indication of trends for shorter layers, but may overpredict the response. Numerical simulations are required to determinehow rapidly the field adjusts after a step. Numerical simulations aregenerally more accurate and more tractable for complex structures,especially for actual 2-dimensional cross-sections of the cores.

BPM and FDTD codes from RSoft Design Group, Inc. were used for numericalsimulations. The BPM algorithm is based on a finite difference beampropagation method. This computation technique uses finite differencemethods to solve the parabolic or paraxial approximation of theHelmholtz equation. The FDTD algorithm is a more rigorous solution toMaxwell's equations and does not contain significant approximations ortheoretical restrictions. This method is widely used as a propagationsolution technique in integrated optics. Numerical simulations of thenew sensor design have centered on waveguide structure optimization,sensitivity analysis, and surface scattering. In most of thecalculations, both BPM and FDTD were employed.

Good sensitivity for the present apparatus requires an adequate detectedpower difference ΔP to provide sufficient signal-to-noise ratios. Thepower difference is usually normalized by P₀, which is taken as thedetected power in the absence of any adlayer. Assuming the targetadlayer thickness before binding is known, the adlayer thickness changeafter binding can be determined from ΔP/P₀. Optimization of core andcladding refractive indices and detector-to-core distance will bediscussed hereinbelow, as will corrections for finite length adlayersand signal-to-noise ratio (SNR).

As stated hereinabove, the analyte solution serves as the upper claddingof the waveguide, but appropriate optical materials for core 16 andlower cladding 14 are now considered. This is a good assumption for thinantigen layers, before the completed antigen/antibody adlayer is formed.FIG. 3 is a contour map for ΔP/P₀ as a function of core and lowercladding refractive indices. It is found that a large ΔP/P₀ may beachieved near cut-off regions. Two waveguide structures have beeninvestigated. The first is a symmetric waveguide, where the core isconstructed from free-standing polyimide materials having n_(c)=1.37. Inthis situation, the upper and lower cladding are made of the aqueousanalyte solutions having n_(u,l)=1.33. In such a structure ΔP/P₀=80% mayreadily be obtained. But fabrication is likely to be difficult due toprocessing procedures necessary to obtain a 100 nm thick freestandingwaveguide. For the second structure, an asymmetric waveguide, the coreis made using SiO_(x)N_(y), where the subscripts x and y indicate thatthe stoichiometry of the core may be adjusted to achieve n=1.8˜2.1.Again, the upper cladding is the aqueous solution with n_(u)=1.33, butnow the lower cladding is made of a solid material such as SiO₂ havingn_(i)=1.45, as an example. It has been found that this waveguide wouldbe easier to fabricate and still offer high sensitivity. In FIG. 3, thesimulation was achieved with the assumption that the adlayer thicknesschanges in the amount of 100 nm, and the detector was placed at adistance S=1 μm from the waveguide core.

FIG. 4 shows the dependence of ΔP/P₀ on detector-to-core distance, S.Two adlayer thickness values have been chosen: 20 nm and 60 nm. In bothsituations, ΔP/P₀ changes exponentially with S which agrees with theEquation 2 hereof. The core index of refraction is 1.8 and the lowercladding index of refraction is 1.45. In general, largerdetector-to-core distances result in a larger ΔP/P₀. However, theabsolute magnitude of P₀ decreases with larger detector-to-coredistances.

Assuming a detector-to-core distance S=1 μm, the dependence of ΔP/P₀ onthe adlayer thickness is shown in FIG. 5. The core index of refractionis assumed to be 1.8 and that for the lower cladding is 1.45.

Although the sensitivity of the sensor for long adlayer patches islarge, the sensitivity decreases when decreasing the length of theadlayer. For finite-length adlayers, the field does not respond rapidlyto changes in the thickness. Two issues are addressed for finite-lengthadlayer detectors: (1) how the finite length adlayer affects the totalsensitivity; and (2) how the field response to one adlayer affects theresponse to a separate adlayer region at another point on the waveguide.It has been determined that the ratio of ΔP(length)/□ΔP(Inf) issubstantially independent of the adlayer thickness as may be observedfrom FIG. 6.

For multiple analyte sensors, numerical simulations have includedinteractions between neighboring sensing regions of the waveguide.Perturbations of the field distribution have been found to exist forsome distance beyond the adlayer. The amplitude of the perturbationdecays approximately exponentially with decay lengths on the order of100 μm.

Another source of noise is surface scattering, Shot noise and thermalnoise in the waveguide can be decreased by using a filter to narrow thebandwidth, giving an signal-to-noise ratio (SNR) of the order of 120 dB.However, surface scattering as a noise source may be the limitingfactor. A waveguide sample surface has been investigated using atomicforce microscopy (AFM) imaging. The roughness of the SiO₂ substrate isRa=0.4 nm˜0.45 nm. The roughness of the core SiO_(x)N_(y) film isRa=0.65 nm˜1.25 nm. An artificial roughness structure has been addedonto the waveguide surface for simulations. SNR due to surface roughnessis plotted in FIG. 7 in a contour plot as a function of detector-to-coredistance, S, and adlayer thickness, d_(a). Waveguide roughness should beminimized using suitable deposition procedures known in the art.Excessive roughness leads both to high loss in the waveguide and to thescattering of light into the detectors which are intended to receiveevanescent light from the waveguide. It may be advantageous that theapproximate roughness of the waveguide is less than the thickness of theadlayer to be detected, for example, less than 10% of this thickness.

A number of SiO_(x)N_(y) films have been deposited on either SiO₂ orglass slips. Waveguides have been patterned via photolithography and dryetching, These waveguide samples are about ≦10 μm in width andapproximately 100 nm in height. To obtain a large light couplingefficiency, the input end of the waveguide has been designed to have atapered structure. Experimental work also has been undertaken oncoupling light into waveguides. The relatively high refractive index ofprototype SiO_(x)N_(y) waveguide samples requires precisely controlledcoupling methods. Both prism and end-fire coupling approaches have beenemployed. An apparatus including a 10 nm-step-resolution piezoelectricxyz translation stage has been assembled and is being used for couplingand positioning. End fire coupling for introducing light into thewaveguide has been employed, where the aligned optical fiber is bondedto the core using epoxy. Fundamental-mode to higher-order modeinterference has also been studied using NSOM which indicates that asingle, guided mode gives rise to the best performance.

In summary, at present, changes in evanescence in waveguides(SiO_(x)N_(y) core with SiO₂ lower cladding) have been measured usingNSOM when layers having n 1.5, such as photoresist material, have beendeposited on the waveguide surface. All other results herein presentedare the product of simulations.

FIG. 8A is a schematic representation of a cross-sectional side view ofan embodiment of the apparatus of the present invention illustratingmultiple sensing locations for detecting a multiplicity of differentanalytes that bind to corresponding recognition layers located on thesurface of the waveguide, while FIG. 8B is a schematic representation ofa top view thereof. The sensor may function by the formation of a singleadlayer 26 a/30 a, or a multiplicity thereof identified as layers 26a/30 a and 26 b/30 b in FIG. 8A, on or near waveguide core 16. Adlayermay consist of proteins or other organic molecules, inorganic particles,metals, combinations of these materials, and materials to be sensedmight be carried to the surface of the waveguide by analyte 24 in liquidor vapor phase. The evanescent field distribution in the upper or lowercladding and thus the power coupling to detector layer 12, shown as amultiplicity of detectors, 12 a, 12 b, opposite corresponding adlayers26 a/30 a and 26 b/30 b, are sensitive to the refractive index andthickness of their corresponding adlayers. The adlayer's refractiveindex may be higher, lower, or equal to the refractive index of thecore. Additional thin layers may be interposed between the waveguidecore and the adlayer so long as those layers permit substantialpenetration of the optical field into the adlayer or analyte. Suchlayers may be useful, for example, for chemical isolation of the analytefrom the core material, modifying the surface properties of the corelayer, or providing chemical specificity.

Chemical specificity of particular adlayers can be provided by placingthin layers of chemical or molecular recognition materials (probespecies) substantially on the waveguide core, as is illustrated by probelayers 26 a and 26 b, which may include DNA, RNA, antibodies, antigens,aptamers, or polymers, gels, or emulsions that react with specific setsof species to be recognized. The use of molecular recognition layers isknown by those skilled in the art of immunoassay and affinity bindingsensors.

FIG. 8A shows recognition (antibody probe) patches 26 a and 26 bimmobilized on waveguide core 16 that can sequester specific targetantigens, as an example, forming thereby layers 30 a and 30 b,respectively, if these species are present in analyte 24. Clearly, agreater number of probe patches can be employed depending on the purposeof the sensor. As an example of the target species specificity of thepresent sensor, if only species, 30 a, which binds to molecularrecognition layer 26a is present, then adlayer 32 would form at 26 a/30a, but not at 26 b/30 b. Additionally, sensor 10 is very sensitive tothe target analyte species, since probe layers 26 a and 26 b can beallowed to “develop” adlayer 32; that is, by permitting analyte 24,containing target species to be sensed, to remain in contact with probelayers 26 a and 26 b for a sufficient amount of time that a detectablequantity of target species is deposited, successful target monitoring orsensing can be achieved using the sensor of the present invention.

Recognition layers can be patterned in lateral extent, and multiples ofsuch layers targeting different species can be position on the samewaveguide core using photolithography, ablation, inkjet printing,scanning probe microscopy, imprint lithography, or other known methodsfor patterning recognition layers. Patterned recognition layers intendedto detect one or more species may be positioned on the same waveguide.As stated hereinabove, when multiple recognition layer regions arepresent that need to be independently detected, the photodetector layer12 may be segmented into regions that substantially correspond in extentalong the length of the waveguide core 16 to the extent of therecognition regions. For example, photodetector segment 12 a wouldprovide a signal principally due to adlayer 26 a/30 a and photodetectorsegment 12 b would provide a signal principally due to adlayer 26 b/30b. Other segments of the photodetector, not shown in FIG. 8A, may not beused for sensing or may be used to provide reference signals whereadlayers do not form. It may be advantageous to provide multipledetector segments in the vicinity of each recognition layer region inorder to perform signal averaging or to determine the rate of change ofthe field, as examples.

FIG. 8B shows a top view of the structure illustrated in FIG. 8A.Electrodes 36 a and 38 a are attached to photodetector segment 12 a,while electrodes 36 b and 38 b are attached to photodetector segment 12b in order to permit analyte measurements. Photocurrents orphotovoltages are measured from these electrodes using conventionalmeasurement apparatus, not shown in FIG. 8B. Such apparatus may includeelectronics formed on a common substrate with the photodetectors. Core16 is shown to have a limited width whereby a single lateral mode ispropagated; that is, in the plane of the wafer, but perpendicular to thedirection of propagation. The photodetector segments extend to bothsides of waveguide core 16. The recognition layer 26 a and correspondingadlayer 30 a regions may or may not be wider than the waveguide as shownin FIG. 8B for regions 30 a/26 a and 30 b/26 b, respectively.

The width of core layer 16 is defined by either completely removing thecore layer in the regions alongside the core forming a rib waveguide orby partially etching them in order to form a ridge waveguide. The widthand type of waveguide can be designed to be multimode or single-mode asunderstood by those skilled in the art of waveguide design. Electrodes,36 a, 38 a, 36 b, and 38 b are separated from core 16 or fabricated fromlow-loss materials so as not to contribute excessive optical loss to thewaveguide, while simultaneously offering acceptable electricalresistance so as not to substantially diminish the electrical signalsfrom photodetectors 12 a and 12 b, respectively.

In one mode of operation, all of the electrodes on one side of thewaveguide, for example, 36 a and 36 b, are biased with one polarity ofvoltage, and all of the electrodes on the opposite side, for example, 38a and 38 b, are biased with the opposite polarity of voltage. In suchsituation, changes in an adlayer region modulate the optical powerabsorbed by the underlying photodetector segment and thus modulates thecurrent flowing from or voltage developed by the correspondingelectrodes. Since only the electrodes on one side the core are requiredto determine the amount of current flowing in the correspondingphotodetector segments, all of the electrodes on the other side of thecore may be electrically connected to a common circuit node to simplifythe wiring. In one embodiment of the invention, the photodetector layeris a semiconductor so that the photodetector acts as a photodiode. Inthis situation, possible photodiode configurations include ametal-semiconductor-metal configuration using lightly doped or undopedsemiconductor and a p-i-n configuration where the photodetector layercontains regions of p-type and n-type doping. Other configurations orphotodiodes may also be used. If electrical isolation is requiredbetween the photodetector segments, insulating regions, 40 a, 40 b, and40 c, may be interposed between the photodetector segments, andsubstrate, 42, may be substantially insulating. Insulating regions 40 a,40 b, and 40 c, may be created by many methods known to those skilled inthe art of photodetector array fabrication including, but not limitedto, ion implantation and etching followed by refilling with aninsulating material.

In actual operation, the majority of the light in the waveguide may beextinguished by the time it reaches the end of the waveguide. However,some light may escape from open end 25, and it may be desirable torecapture this escaped radiation to reduce the possibility of scatteringback into the system when the apparatus 10 is placed in a solutioncontaining analyte 24. It is not necessary for device operation thatthis is done, but it may be desirable to place reflection reducingmaterials, such as anti-reflection coatings, absorber layers, angledfacets, waveguide bends, or other means known to those practiced in theart of waveguide engineering to reduce reflections at the end of thewaveguide.

It is to be mentioned that multiple waveguides may be employed foranalyte analysis. By use of waveguide splitters and bends, light from asingle optical source can be transmitted to multiple, non-intersectingwaveguide segments, each of which might contain multiple sensingregions. In this manner, additional sensor regions could be providedwithout significantly increasing the complexity of the light coupling.Moreover, the additional waveguide structures might be used for sensingadditional analytes.

In “Direct Imaging of Transient Interference in a Single-Mode WaveguideUsing Near-Field Scanning Optical Microscopy” by Guangwei Yuan, supra,it is stated that near-field scanning optical microscopy was used toimage transient interference between the guided mode and a leaky modeinduced in a single-mode waveguide due to a localized adlayer. Suchinterference may impact the element spacing for the sensors of thepresent invention and sufficient spacing between sensitization elementsmay allow such oscillations to decay. One may also attempt to minimizestep heights associated with the sensitization layer in the absence ofthe analyte under investigation.

A longitudinal change of refractive index in isolated detectors belowthe waveguide is likely to have the same effect. Therefore, a continuouslayer of photodetector material with many electrical contacts, all tothe same piece of silicon or other detector material may generateimproved performance for the light coupling embodiment of the presentinvention. Implants, diffusion, or other processes known to alter theconductivity between the elements of the continuous detector materialmay be useful to electrically isolate them from one another in somecases, but it is not clear that this is necessary. Such processes areexpected to have only small effects on the refractive index propertiesof the material and could be engineered to trade off minimal disruptionof the optical field with adequate isolation if any is required.

The foregoing description of the invention has been presented forpurposes of illustration and description and is not intended to beexhaustive or to limit the invention to the precise form disclosed, andobviously many modifications and variations are possible in light of theabove teaching. The embodiments were chosen and described in order tobest explain the principles of the invention and its practicalapplication to thereby enable others skilled in the art to best utilizethe invention in various embodiments and with various modifications asare suited to the particular use contemplated. It is intended that thescope of the invention be defined by the claims appended hereto.

What is claimed is:
 1. A method for detecting an analyte, comprising thesteps of: introducing light having a chosen wavelength or band ofwavelengths into an optical guide having a first surface and an axis,capable of transmitting light along the axis, and having at least oneregion in the vicinity of the surface thereof wherein the refractiveindex thereof is altered by the presence of the analyte; placing theanalyte in the vicinity of the at least one region of the first surface,whereby the intensity of the light coupled out of the optical guide ischanged as a result of the presence of the analyte; and detecting thechange of intensity of the light coupled out of the guide at the chosenwavelength or band of wavelengths in the vicinity of the at least oneregion.
 2. The method of claim 1, wherein the optical guide guides asingle mode of the light at close to cut-off independent of the presenceof the analyte.
 3. The method of claim 1, wherein the optical guide issubstantially rectangular.
 4. The method of claim 3, wherein the singlemode comprises the TE₀ mode.
 5. The method of claim 1, wherein said stepof detecting the change of intensity of the light coupled out of theoptical guide is performed on the side of the optical guide opposite theside on which the at least one region of the first surface is located.6. The method of claim 1, wherein said step of detecting the change ofintensity of the light coupled out of the optical guide is performed onthe same side of the optical guide as the at least one region of thefirst surface is located.
 7. The method of claim 6, wherein said step ofdetecting the change of intensity of the light coupled out of theoptical guide is performed on the same side of said optical guide as theat least one region of the first surface of said optical guide islocated and separated therefrom by the analyte.
 8. The method of claim1, wherein the analyte is dissolved in a solvent.
 9. The method of claim1, wherein at least one probe species is immobilized on the at least oneregion of the first surface of the optical guide, and the analytecontains target species capable of binding to the at least one probespecies.
 10. The method of claim 1, wherein the optical guide furthercomprises a second surface opposite the first surface thereof, andwherein a cladding layer is disposed substantially contiguous with thesecond surface.